taxizedb
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ropensci
children test failing
the test at https://github.com/ropensci/taxizedb/blob/master/tests/testthat/test-children.R#L10-L13 is failing
I see
taxize::children(3701, db='ncbi')
#> $`3701`
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 1837063 Arabidopsis thaliana x Arabidopsis halleri species
#> 2 1746102 Arabidopsis sp. hda9-2 species
#> 3 1547873 Arabidopsis sp. NH-2014a species
#> 4 1547872 Arabidopsis umezawana species
#> 5 1328956 (Arabidopsis thaliana x Arabidopsis arenosa) x Arabidopsis suecica species
#> 6 1240361 Arabidopsis thaliana x Arabidopsis arenosa species
#> 7 869751 Arabidopsis thaliana x Arabidopsis halleri subsp. gemmifera species
#> 8 869750 Arabidopsis thaliana x Arabidopsis lyrata species
#> 9 412662 Arabidopsis pedemontana species
#> 10 378006 Arabidopsis arenosa x Arabidopsis thaliana species
#> 11 347883 Arabidopsis arenicola species
#> 12 302551 Arabidopsis petrogena species
#> 13 97980 Arabidopsis croatica species
#> 14 97979 Arabidopsis cebennensis species
#> 15 81970 Arabidopsis halleri species
#> 16 59690 Arabidopsis kamchatica species
#> 17 59689 Arabidopsis lyrata species
#> 18 45251 Arabidopsis neglecta species
#> 19 45249 Arabidopsis suecica species
#> 20 38785 Arabidopsis arenosa species
#> 21 29726 Arabidopsis sp. species
#> 22 3702 Arabidopsis thaliana species
#>
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "ncbi"
taxizedb::children(3701, db='ncbi')
#> $`3701`
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 1837063 Arabidopsis thaliana x Arabidopsis halleri species
#> 2 1547872 Arabidopsis umezawana species
#> 3 1328956 (Arabidopsis thaliana x Arabidopsis arenosa) x Arabidopsis suecica species
#> 4 1240361 Arabidopsis thaliana x Arabidopsis arenosa species
#> 5 869750 Arabidopsis thaliana x Arabidopsis lyrata species
#> 6 412662 Arabidopsis pedemontana species
#> 7 378006 Arabidopsis arenosa x Arabidopsis thaliana species
#> 8 347883 Arabidopsis arenicola species
#> 9 302551 Arabidopsis petrogena species
#> 10 97980 Arabidopsis croatica species
#> 11 97979 Arabidopsis cebennensis species
#> 12 81970 Arabidopsis halleri species
#> 13 59690 Arabidopsis kamchatica species
#> 14 59689 Arabidopsis lyrata species
#> 15 45251 Arabidopsis neglecta species
#> 16 45249 Arabidopsis suecica species
#> 17 38785 Arabidopsis arenosa species
#> 18 3702 Arabidopsis thaliana species
#>
#> attr(,"class")
#> [1] "children"
#> attr(,"db")
#> [1] "ncbi"
:p> packageVersion('taxize')
[1] ‘0.9.4.9914’
:p> packageVersion('taxizedb')
[1] ‘0.1.7.9602’
@sckott Looks like an issue with the ambiguous flag:
These are equal:
taxizedb::children(3701, db='ncbi', ambiguous=TRUE)
taxize::children(3701, db='ncbi', ambiguous=TRUE)
And so are these:
taxizedb::children(3701, db='ncbi', ambiguous=FALSE)
taxize::children(3701, db='ncbi', ambiguous=FALSE)
But not these:
taxizedb::children(3701, db='ncbi')
taxize::children(3701, db='ncbi')
Judging by the output above, in taxize the default is ambiguous=TRUE and in taxizedb it is ambiguous=FALSE.
I think something is mixed up on the taxize side. According to ?taxize::ncbi_children, ambiguous is FALSE by default. Yet somewhere the default appears to be overridden.
What do you think about this set of test:
# they agree in the ambiguous case
expect_equal(
taxizedb::children(3701, db='ncbi', ambiguous=TRUE),
taxize::children(3701, db='ncbi', ambiguous=TRUE)
)
# they agree in the unambiguous case
expect_equal(
taxizedb::children(3701, db='ncbi', ambiguous=FALSE),
taxize::children(3701, db='ncbi', ambiguous=FALSE)
)
# the defaults agree
expect_equal(
taxizedb::children(3701, db='ncbi'),
taxize::children(3701, db='ncbi')
)
Currently, the last test fails, but I think the default behavior of taxize and taxizedb should be the same.
